I have a BAM file that has 170X whole exome coverage.
I would like to create a new BAM file from the original that has 100X genome coverage.
I know samtools view -s option will give me the result but what float digit I should give to get 100X coverage?
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nalesh_jadhav •
-s FLOAT subsample reads (given INT.FRAC option value, 0.FRAC is the
fraction of templates/read pairs to keep; INT part sets seed)
So 100/170 = 0.59 so you want to keep 59% of all reads, therefore use e.g. -s 1.59 where the .59 is the fraction to keep and the 1 is a random seed for reproducibility.
Thank you for the quick reply. That was completely correct and I got the required result.
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